Contacts of the helix formed by residues 736 - 751 (chain F) in PDB entry 5G04
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 736 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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707F PHE* 6.6 0.2 - - + -
733F VAL* 3.5 27.4 + - + +
734F PRO 3.4 3.1 - - - +
735F LYS* 1.3 76.7 - - - +
737F SER* 1.3 68.3 + - - +
738F LEU* 3.3 21.8 + - + +
739F VAL* 3.6 37.3 + - + +
740F TYR* 3.8 12.0 + - - -
766F LEU* 5.0 0.2 - - - -
492R SER 4.1 13.0 + - - -
493R LEU* 3.9 15.6 + - + +
494R ILE* 3.4 29.3 - - + +
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Residues in contact with SER 737 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735F LYS 3.4 4.7 + - - -
736F GLU* 1.3 78.9 - - - +
738F LEU* 1.3 59.8 + - - +
740F TYR* 3.2 5.1 + - - +
741F PHE* 3.0 26.4 + - - +
763F ALA* 3.4 29.8 + - - +
766F LEU* 4.3 13.5 - - - -
767F ASP* 3.8 24.6 - - - +
770F GLY 5.4 2.1 + - - -
771F ALA* 5.8 0.5 - - - -
774F GLN* 5.3 7.3 - - - +
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Residues in contact with LEU 738 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707F PHE* 4.2 24.2 - - + -
736F GLU* 3.3 15.7 + - + +
737F SER* 1.3 77.9 - - - +
739F VAL* 1.3 57.8 + - - +
741F PHE* 3.7 14.3 - - + +
742F LEU* 2.7 38.2 + - + +
770F GLY 5.7 0.2 - - - +
773F ASN 5.6 1.1 - - - +
774F GLN* 3.8 34.3 - - + -
777F GLU* 4.0 23.1 - - + -
494R ILE* 3.5 35.7 - - + -
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Residues in contact with VAL 739 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707F PHE* 4.5 5.7 - - + -
726F LEU* 4.0 22.4 - - + +
729F LEU* 3.4 31.9 - - + -
730F LYS* 4.3 13.9 - - + +
733F VAL* 4.2 10.1 - - + +
736F GLU* 3.6 31.9 - - + +
738F LEU* 1.3 77.5 - - - +
740F TYR* 1.3 64.0 + - + +
742F LEU* 3.3 1.9 + - - +
743F ILE* 2.9 51.6 + - + +
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Residues in contact with TYR 740 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730F LYS* 3.5 42.2 - - + +
734F PRO* 3.2 28.9 + - - +
736F GLU 3.8 8.9 + - - -
737F SER* 3.2 7.8 + - - +
739F VAL* 1.3 83.2 - - + +
741F PHE* 1.3 61.5 + - - +
743F ILE* 3.3 8.0 + - + -
744F GLY 3.1 17.3 + - - -
759F ASN* 3.4 41.6 - - - +
762F TRP* 3.7 26.8 - + + -
763F ALA 4.1 8.3 - - - +
766F LEU* 3.6 28.5 - - + -
144J ASP* 5.7 1.0 + - - -
146J ARG* 5.8 1.0 + - - -
362J GLN* 4.7 16.5 + - - +
365J LYS* 5.7 2.4 + - - -
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Residues in contact with PHE 741 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737F SER* 3.0 16.9 + - - +
738F LEU* 3.7 19.7 - - + +
740F TYR* 1.3 75.8 - - - +
742F LEU* 1.3 68.8 + - + +
744F GLY* 3.1 11.8 + - - -
745F LYS* 3.2 50.7 + - + +
759F ASN 4.8 2.0 - - - -
760F PHE* 4.1 30.9 - + - +
763F ALA* 3.8 21.6 - - + +
771F ALA 5.9 0.4 - - - -
774F GLN* 4.2 33.9 - - + -
775F ILE* 5.6 1.3 - - - -
777F GLU* 6.3 0.2 - - + -
778F ALA* 4.8 3.6 - - + -
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Residues in contact with LEU 742 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707F PHE* 3.4 30.3 - - + -
710F ALA* 4.5 13.2 - - + +
711F SER* 4.1 25.1 - - - +
714F PHE* 4.8 10.5 - - + -
726F LEU* 3.7 29.8 - - + -
738F LEU 2.7 22.5 + - - +
739F VAL 3.7 2.7 - - - +
741F PHE* 1.3 78.8 - - + +
743F ILE* 1.3 62.8 + - - +
745F LYS* 3.1 20.0 + - + +
746F VAL* 3.2 19.7 + - + +
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Residues in contact with ILE 743 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723F LEU* 3.8 24.2 - - + -
726F LEU* 3.7 33.9 - - + +
727F GLU* 5.1 4.5 - - + +
730F LYS* 3.8 28.0 - - - +
739F VAL* 2.9 46.6 + - + +
740F TYR* 3.8 9.9 - - + +
742F LEU* 1.3 73.3 - - - +
744F GLY* 1.3 62.0 - - - +
746F VAL* 3.2 5.3 + - - +
747F TYR* 3.2 26.6 + - + -
759F ASN* 3.3 21.1 - - - +
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Residues in contact with GLY 744 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740F TYR 3.1 10.5 + - - -
741F PHE 3.1 5.6 + - - -
743F ILE* 1.3 76.1 - - - +
745F LYS* 1.3 60.2 + - - +
747F TYR* 3.3 3.9 + - - +
748F LYS* 3.1 19.1 + - - +
756F ALA* 3.9 9.0 - - - +
759F ASN* 3.6 21.8 - - - +
760F PHE* 3.4 23.9 - - - -
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Residues in contact with LYS 745 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714F PHE* 3.5 29.6 - - + -
741F PHE* 3.2 40.0 + - + +
742F LEU* 3.1 15.6 + - + +
744F GLY* 1.3 75.0 - - - +
746F VAL* 1.3 63.2 + - - +
748F LYS* 3.4 21.9 + - + +
749F LYS* 3.6 6.2 + - - +
760F PHE* 3.7 16.7 - - + -
778F ALA* 3.2 37.4 + - - +
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Residues in contact with VAL 746 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714F PHE* 3.6 22.4 - - + -
719F TYR* 4.0 31.1 - - + +
722F ALA* 4.7 6.7 - - + -
723F LEU* 3.8 28.7 - - + -
726F LEU* 3.8 23.3 - - + -
742F LEU* 3.2 19.4 + - + +
743F ILE 3.2 5.8 + - - +
745F LYS* 1.3 75.0 - - - +
747F TYR* 1.3 61.4 + - - +
749F LYS* 3.2 16.6 + - - +
750F LEU* 3.2 13.0 + - + +
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Residues in contact with TYR 747 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723F LEU* 3.6 36.3 - - + +
727F GLU* 4.4 9.4 + - - -
743F ILE* 3.2 19.0 + - + +
744F GLY 3.3 2.0 + - - +
746F VAL* 1.3 74.1 - - - +
748F LYS* 1.3 54.0 + - - +
750F LEU* 3.0 11.3 + - + -
751F GLY 2.7 32.4 + - - -
752F GLN* 3.5 34.0 + - - +
755F LEU* 3.6 40.9 - - + +
756F ALA* 3.8 21.5 - - + +
759F ASN* 3.6 29.2 - - - -
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Residues in contact with LYS 748 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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744F GLY 3.1 13.1 + - - +
745F LYS* 3.6 15.5 - - + +
746F VAL 3.3 0.2 - - - -
747F TYR* 1.3 74.4 - - - +
749F LYS* 1.3 59.6 + - + +
751F GLY* 3.0 21.0 + - - +
753F THR* 6.1 3.8 - - + +
756F ALA* 3.9 15.1 - - + +
760F PHE* 4.2 24.7 - - + -
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Residues in contact with LYS 749 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714F PHE* 4.1 23.1 - - + -
717F GLU* 4.3 11.4 + - - -
719F TYR* 3.4 47.1 - - + +
745F LYS 3.8 13.0 - - - +
746F VAL 3.2 8.4 + - - +
748F LYS* 1.3 78.6 - - + +
750F LEU* 1.3 59.5 + - - +
751F GLY* 3.5 0.9 + - - -
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Residues in contact with LEU 750 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719F TYR* 4.0 30.7 - - + -
720F LYS 5.7 0.4 - - - +
723F LEU* 3.8 22.9 - - + -
746F VAL* 3.2 13.2 + - + +
747F TYR* 3.0 31.7 + - + +
749F LYS* 1.3 75.5 - - - +
751F GLY* 1.3 57.3 + - - +
752F GLN* 3.3 25.0 + - + +
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Residues in contact with GLY 751 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747F TYR 2.7 11.9 + - - -
748F LYS 3.0 15.4 + - - -
749F LYS 3.2 1.1 - - - -
750F LEU* 1.3 73.6 - - - +
752F GLN* 1.3 51.5 + - - -
753F THR* 2.8 31.0 + - - +
389J ARG* 5.0 9.6 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il